Every taxi I've ever ridden in clearly lays out the initial charge, how much distance is included, how much additional distance is charged, how much idle time is charged, and any additional fees.
I've also had drivers in SF smoke, refuse to give me a ride, and try to charge me extra fees, all of which are, AFAIK, against the law.
Fortunately, the law protects you again in this case. In NYC (and SF too, I believe), if the credit card machine doesn't work, and the cab driver doesn't tell you before you start the ride, you don't have to pay a dime.